I think it actually might be stand-alone.. just because of all the animation they'd need to fill. Or have the option come after you download content. Dunno how many skeleton types there are going to be in this pokemon world, but a few might be shared like in Stadium. We'll have to see!

Well seeing as all Transferring does is Transfer the Statistics of a Pokemon and the Species Name of the Pokemon I can't see it being all that hard to Allow us to Migrate

All it has to do is Apply those Statistics to the 3D Model of the Species Name that was Transferred
And I Highly Doubt they will Revamp IV's Like they did in Gen III
(The IV Revamping was the Reason you couldn't migrate plus You Couldn't Link a GBC to a GBA)